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Detailed information for vg0314583769:

Variant ID: vg0314583769 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14583769
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GCATGTTTACGAAATGACATATCACATATTGATCTATCCTACTGAATTTTTTCATTTTTAATGATTTTTTTTAAGTTACATTCACTGGTGGAGAAACCAT[T/C]
TTTGCTCGGTCAACCCAAATCCACAGTAGTCCTGGTTCCACTAAAAACCGAGAGTAAAAACGATTTTTAGTCCCGGTTTATAAGAACAACAGGACTAGAT

Reverse complement sequence

ATCTAGTCCTGTTGTTCTTATAAACCGGGACTAAAAATCGTTTTTACTCTCGGTTTTTAGTGGAACCAGGACTACTGTGGATTTGGGTTGACCGAGCAAA[A/G]
ATGGTTTCTCCACCAGTGAATGTAACTTAAAAAAAATCATTAAAAATGAAAAAATTCAGTAGGATAGATCAATATGTGATATGTCATTTCGTAAACATGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.20%	32.60%	0.21%	0.00%	NA
All Indica	2759	55.40%	44.30%	0.33%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	51.10%	48.60%	0.34%	0.00%	NA
Indica II	465	27.30%	72.30%	0.43%	0.00%	NA
Indica III	913	74.90%	24.90%	0.22%	0.00%	NA
Indica Intermediate	786	52.50%	47.10%	0.38%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0314583769	T -> C	LOC_Os03g25530.1	downstream_gene_variant ; 4523.0bp to feature; MODIFIER	silent_mutation	Average:28.612; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0314583769	T -> C	LOC_Os03g25540.1	downstream_gene_variant ; 776.0bp to feature; MODIFIER	silent_mutation	Average:28.612; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0314583769	T -> C	LOC_Os03g25540-LOC_Os03g25550	intergenic_region ; MODIFIER	silent_mutation	Average:28.612; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314583769	4.90E-49	1.20E-113	mr1542	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0314583769	5.35E-41	1.02E-62	mr1542	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0314583769	NA	1.48E-08	mr1902	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0314583769	6.13E-06	4.09E-19	mr1281_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0314583769	3.23E-51	1.08E-124	mr1542_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0314583769	6.91E-50	1.19E-71	mr1542_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0314583769	2.67E-13	9.71E-33	mr1587_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0314583769	8.61E-15	3.55E-20	mr1587_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251